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added a new Makefile for simde
1 parent 66db9da commit ccb0f7b

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-38
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3 files changed

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Diff for: ‎Makefile

+5-34
Original file line numberDiff line numberDiff line change
@@ -1,40 +1,26 @@
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CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
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CPPFLAGS= -DHAVE_KALLOC
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INCLUDES=
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
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PROG= minimap2
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PROG_EXTRA= sdust minimap2-lite
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LIBS= -lm -lz -lpthread
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9-
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ifeq ($(no_simd),) # if no_simd is not defined
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ifeq ($(arm_neon),) # if arm_neon is not defined
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OBJS+=ksw2_ll_sse.o
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ifeq ($(sse2only),) # if sse2only is not defined
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OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
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else # if sse2only is defined
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OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
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endif
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else # if arm_neon is defined
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OBJS+=ksw2_ll_neon.o ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
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ifeq ($(simde),) # arm_neon without SIMDe -> use sse2neon
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INCLUDES+=-Isse2neon
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endif
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OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
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INCLUDES+=-Isse2neon
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ifeq ($(aarch64),) #if aarch64 is not defined
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CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
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else #if aarch64 is defined
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CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
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endif
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endif
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else
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OBJS+=ksw2_ll_nosimd.o ksw2_extz2_nosimd.o ksw2_extd2_nosimd.o ksw2_exts2_nosimd.o
31-
simde=1 # no_simd can be used only with SIMDe
32-
endif
33-
34-
ifneq ($(simde),) # if simde is defined
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CFLAGS+=-DSIMDE_ENABLE_NATIVE_ALIASES -DUSE_SIMDE
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INCLUDES+=-Ilib/simde
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endif
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3925
ifneq ($(asan),)
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CFLAGS+=-fsanitize=address
@@ -70,8 +56,10 @@ sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
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# SSE-specific targets on x86/x86_64
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59+
ifeq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)
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ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
62+
endif
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ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
@@ -96,9 +84,6 @@ ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
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# NEON-specific targets on ARM
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99-
ksw2_ll_neon.o:ksw2_ll_sse.c ksw2.h kalloc.h
100-
$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
101-
10287
ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
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@@ -108,20 +93,6 @@ ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
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111-
# no-SIMD version
112-
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ksw2_ll_nosimd.o:ksw2_ll_sse.c ksw2.h kalloc.h
114-
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
115-
116-
ksw2_extz2_nosimd.o:ksw2_extz2_sse.c ksw2.h kalloc.h
117-
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
118-
119-
ksw2_extd2_nosimd.o:ksw2_extd2_sse.c ksw2.h kalloc.h
120-
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
121-
122-
ksw2_exts2_nosimd.o:ksw2_exts2_sse.c ksw2.h kalloc.h
123-
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
124-
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# other non-file targets
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clean:

Diff for: ‎Makefile.simde

+97
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,97 @@
1+
CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
2+
CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
3+
INCLUDES= -Ilib/simde
4+
OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o \
5+
ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
6+
PROG= minimap2
7+
PROG_EXTRA= sdust minimap2-lite
8+
LIBS= -lm -lz -lpthread
9+
10+
11+
ifneq ($(arm_neon),) # if arm_neon is defined
12+
ifeq ($(aarch64),) #if aarch64 is not defined
13+
CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
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else #if aarch64 is defined
15+
CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
16+
endif
17+
endif
18+
19+
ifneq ($(asan),)
20+
CFLAGS+=-fsanitize=address
21+
LIBS+=-fsanitize=address
22+
endif
23+
24+
ifneq ($(tsan),)
25+
CFLAGS+=-fsanitize=thread
26+
LIBS+=-fsanitize=thread
27+
endif
28+
29+
.PHONY:all extra clean depend
30+
.SUFFIXES:.c .o
31+
32+
.c.o:
33+
$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
34+
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all:$(PROG)
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extra:all $(PROG_EXTRA)
38+
39+
minimap2:main.o libminimap2.a
40+
$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
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minimap2-lite:example.o libminimap2.a
43+
$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
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45+
libminimap2.a:$(OBJS)
46+
$(AR) -csru $@ $(OBJS)
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48+
sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
49+
$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
50+
51+
ksw2_ll_simde.o:ksw2_ll_sse.c ksw2.h kalloc.h
52+
$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
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54+
ksw2_extz2_simde.o:ksw2_extz2_sse.c ksw2.h kalloc.h
55+
$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
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57+
ksw2_extd2_simde.o:ksw2_extd2_sse.c ksw2.h kalloc.h
58+
$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
59+
60+
ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
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63+
# other non-file targets
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clean:
66+
rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
67+
68+
depend:
69+
(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
70+
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# DO NOT DELETE
72+
73+
align.o: minimap.h mmpriv.h bseq.h kseq.h ksw2.h kalloc.h
74+
bseq.o: bseq.h kvec.h kalloc.h kseq.h
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chain.o: minimap.h mmpriv.h bseq.h kseq.h kalloc.h
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esterr.o: mmpriv.h minimap.h bseq.h kseq.h
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example.o: minimap.h kseq.h
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format.o: kalloc.h mmpriv.h minimap.h bseq.h kseq.h
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hit.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h khash.h
80+
index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h kvec.h kalloc.h khash.h
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index.o: ksort.h
82+
kalloc.o: kalloc.h
83+
ksw2_extd2_sse.o: ksw2.h kalloc.h
84+
ksw2_exts2_sse.o: ksw2.h kalloc.h
85+
ksw2_extz2_sse.o: ksw2.h kalloc.h
86+
ksw2_ll_sse.o: ksw2.h kalloc.h
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kthread.o: kthread.h
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main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h
89+
map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h kseq.h
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map.o: khash.h ksort.h
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misc.o: mmpriv.h minimap.h bseq.h kseq.h ksort.h
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options.o: mmpriv.h minimap.h bseq.h kseq.h
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pe.o: mmpriv.h minimap.h bseq.h kseq.h kvec.h kalloc.h ksort.h
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sdust.o: kalloc.h kdq.h kvec.h sdust.h
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self-chain.o: minimap.h kseq.h
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sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h kseq.h
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splitidx.o: mmpriv.h minimap.h bseq.h kseq.h

Diff for: ‎README.md

+8-4
Original file line numberDiff line numberDiff line change
@@ -80,11 +80,14 @@ directory to compile. If you see compilation errors, try `make sse2only=1`
8080
to disable SSE4 code, which will make minimap2 slightly slower.
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8282
Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To
83-
compile for 32 bit ARM architectures (such as ARMv7), use `make arm_neon=1`. To compile for for 64 bit ARM architectures (such as ARMv8), use `make arm_neon=1 aarch64=1`.
83+
compile for 32 bit ARM architectures (such as ARMv7), use `make arm_neon=1`. To
84+
compile for for 64 bit ARM architectures (such as ARMv8), use `make arm_neon=1
85+
aarch64=1`.
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85-
Minimap2 can use [SIMD Everywhere (SIMDe)](https://github.com/nemequ/simde) library for porting implementation
86-
to the different SIMD instruction sets. To compile using SIMDe, use `make simde=1`. To compile for ARM CPUs, add `simde=1` to the commands given above.
87-
SIMDe also enables non-SIMD implementation using `make no_simd=1`.
87+
Minimap2 can use [SIMD Everywhere (SIMDe)][simde] library for porting
88+
implementation to the different SIMD instruction sets. To compile using SIMDe,
89+
use `make -f Makefile.simde`. To compile for ARM CPUs, use `Makefile.simde`
90+
with the ARM related command lines given above.
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### <a name="general"></a>General usage
9093

@@ -380,3 +383,4 @@ mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
380383
[manpage]: https://lh3.github.io/minimap2/minimap2.html
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[manpage-cs]: https://lh3.github.io/minimap2/minimap2.html#10
382385
[doi]: https://doi.org/10.1093/bioinformatics/bty191
386+
[smide]: https://github.com/nemequ/simde

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